Skip to content

Issues: gerlichlab/looptrace

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

163 Open 185 Closed
163 Open 185 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Iteration over subpixel localization arguments yields incorrect timepoints, in general, when using locus grouping blocking bug Something isn't working configuration priority high
#420 opened Jan 23, 2025 by vreuter v0.12
@vreuter
Visualisations for various record counts by trace group brainstorming question Further information is requested visualisation
#419 opened Jan 22, 2025 by vreuter
@vreuter @TLSteinacker
2
Consider changes to regional spots' pairwise distances program
#417 opened Jan 18, 2025 by vreuter v0.13
Regional spots' pairwise distances program can lead to OutOfMemory error pipeline
#416 opened Jan 18, 2025 by vreuter v0.13
Turning off spot filtration by nuclei (Setting spot_in_nuc to False) breaks spot counts visualisation configuration pipeline
#415 opened Jan 17, 2025 by vreuter v0.13
@vreuter
Table parse crashes when file (data frame) is empty bug Something isn't working likely solved pipeline
#414 opened Jan 17, 2025 by vreuter v0.12
@vreuter
Forgetting pixelSeparationBeneathWhichSpotRoisWillMerge key in the parameters configuration file fails to be caught in pipeline precheck bug Something isn't working configuration likely solved pipeline
#413 opened Jan 17, 2025 by vreuter v0.12
@vreuter
Failure to parse, during ImageHandler intialization`, any content of analysis subfolder results in logging warning likely solved
#412 opened Jan 17, 2025 by vreuter v0.12
@vreuter
ImageHandler aggression: parsing contents of analysis subfolder pipeline umbrella
#411 opened Jan 17, 2025 by vreuter
1 of 2 tasks
@vreuter
reg_ref_frame use isn't caught by pipeline_precheck bug Something isn't working configuration likely solved
#410 opened Jan 17, 2025 by vreuter v0.12
@vreuter
Consider / Confirm: require locusGrouping section if doing ROI merge for tracing (mergeRulesForTracing section) configuration
#409 opened Jan 10, 2025 by vreuter v0.13
@vreuter
Omit voxel for regional timepoint from locus spot visualization stack
#408 opened Jan 3, 2025 by vreuter v0.12.1
@vreuter
1
Track/store reindexed trace ID (for each FOV or (FOV, trace group) value) enhancement New feature or request visualisation
#407 opened Dec 19, 2024 by vreuter v0.12.1
@vreuter
Track/store the reindexed (0-based) locus timepoints (per FOV or (FOV, trace group) combination) enhancement New feature or request visualisation
#406 opened Dec 19, 2024 by vreuter
1 task
v0.12.1
@vreuter
Deprecate empirical point-spread function (PSF) determination configuration documentation Improvements or additions to documentation
#405 opened Dec 19, 2024 by vreuter
3 tasks
v0.13
@vreuter
Visualisation of tracing structures enhancement New feature or request visualisation
#404 opened Dec 7, 2024 by vreuter v0.13
@vreuter
Switching to TetraSpeck beads umbrella
#403 opened Dec 6, 2024 by vreuter
2 tasks
v0.13
@vreuter
Changes to locus spot visualisation enhancement New feature or request umbrella visualisation
#402 opened Dec 6, 2024 by vreuter
1 of 4 tasks
v0.12.1
@vreuter
Apply proximity filter between beads and FISH spots enhancement New feature or request
#401 opened Dec 6, 2024 by vreuter v0.13
@vreuter
Mask out TetraSpeck beads with nucler regions enhancement New feature or request
#400 opened Dec 6, 2024 by vreuter v0.13
@vreuter
Prioritise trace group/structure name and locus timepoints for sorting records in locus pairwise distances enhancement New feature or request likely solved
#396 opened Dec 2, 2024 by vreuter
2 tasks done
v0.12
@vreuter
Test that no duplication of records is done in locus pairwise distances likely solved testing
#395 opened Dec 2, 2024 by vreuter v0.12
@vreuter
Restructuring data-driven tests for better encapsulation and less fragility good first issue Good for newcomers help wanted Extra attention is needed testing
#394 opened Dec 1, 2024 by vreuter
Add test that each timepoint to merge for tracing is regional likely solved testing
#393 opened Dec 1, 2024 by vreuter v0.12
@vreuter
Make the encounter of a pair of records with the same locus time within the same trace an error likely solved
#392 opened Nov 29, 2024 by vreuter
1 task done
v0.12
@vreuter
ProTip! Mix and match filters to narrow down what you’re looking for.